Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.)

Sujay, V.; Gowda, M. V. C.; Pandey, M. K.; Bhat, R. S.; Khedikar, Y. P.; Nadaf, H. L.; Gautami, B.; Sarvamangala, C.; Lingaraju, S.; Radhakrishan, T.; Knapp, S. J.; Varshney, R. K.

doi:10.1007/s11032-011-9661-z

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Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut ( Arachis hypogaea L.)

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Author(s): V. Sujay ¹ ^, ² , M. V. C. Gowda ² , M. K. Pandey ¹ , R. S. Bhat ³ , Y. P. Khedikar ¹ ^, ² , H. L. Nadaf ² , B. Gautami ¹ , C. Sarvamangala ² , S. Lingaraju ⁴ , T. Radhakrishan ⁵ , S. J. Knapp ⁶ , R. K. Varshney ¹ ^, ⁷ ^,

Publication date (Electronic): 22 November 2011

Journal: Molecular Breeding

Publisher: Springer Netherlands

Keywords: Genetic linkage map, Rust resistance, Late leaf spot resistance, Molecular breeding, Molecular markers

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Abstract

Late leaf spot (LLS) and rust have the greatest impact on yield losses worldwide in groundnut ( Arachis hypogaea L.). With the objective of identifying tightly linked markers to these diseases, a total of 3,097 simple sequence repeats (SSRs) were screened on the parents of two recombinant inbred line (RIL) populations, namely TAG 24 × GPBD 4 (RIL-4) and TG 26 × GPBD 4 (RIL-5), and segregation data were obtained for 209 marker loci for each of the mapping populations. Linkage map analysis of the 209 loci resulted in the mapping of 188 and 181 loci in RIL-4 and RIL-5 respectively. Using 143 markers common to the two maps, a consensus map with 225 SSR loci and total map distance of 1,152.9 cM was developed. Comprehensive quantitative trait locus (QTL) analysis detected a total of 28 QTL for LLS and 15 QTL for rust. A major QTL for LLS, namely QTL _LLS01 (GM1573/GM1009-pPGPseq8D09), with 10.27–62.34% phenotypic variance explained (PVE) was detected in all the six environments in the RIL-4 population. In the case of rust resistance, in addition to marker IPAHM103 identified earlier, four new markers (GM2009, GM1536, GM2301 and GM2079) showed significant association with the major QTL (82.96% PVE). Localization of 42 QTL for LLS and rust on the consensus map identified two candidate genomic regions conferring resistance to LLS and rust. One region present on linkage group AhXV contained three QTL each for LLS (up to 67.98% PVE) and rust (up to 82.96% PVE). The second candidate genomic region contained the major QTL with up to 62.34% PVE for LLS. Molecular markers associated with the major QTL for resistance to LLS and rust can be deployed in molecular breeding for developing groundnut varieties with enhanced resistance to foliar diseases.

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Precision mapping of quantitative trait loci.

Z. -B. Zeng (1994)

Adequate separation of effects of possible multiple linked quantitative trait loci (QTLs) on mapping QTLs is the key to increasing the precision of QTL mapping. A new method of QTL mapping is proposed and analyzed in this paper by combining interval mapping with multiple regression. The basis of the proposed method is an interval test in which the test statistic on a marker interval is made to be unaffected by QTLs located outside a defined interval. This is achieved by fitting other genetic markers in the statistical model as a control when performing interval mapping. Compared with the current QTL mapping method (i.e., the interval mapping method which uses a pair or two pairs of markers for mapping QTLs), this method has several advantages. (1) By confining the test to one region at a time, it reduces a multiple dimensional search problem (for multiple QTLs) to a one dimensional search problem. (2) By conditioning linked markers in the test, the sensitivity of the test statistic to the position of individual QTLs is increased, and the precision of QTL mapping can be improved. (3) By selectively and simultaneously using other markers in the analysis, the efficiency of QTL mapping can be also improved. The behavior of the test statistic under the null hypothesis and appropriate critical value of the test statistic for an overall test in a genome are discussed and analyzed. A simulation study of QTL mapping is also presented which illustrates the utility, properties, advantages and disadvantages of the method.

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Genomics-assisted breeding for crop improvement.

Rajeev Varshney, Andreas Graner, Mark E. Sorrells (2005)

Genomics research is generating new tools, such as functional molecular markers and informatics, as well as new knowledge about statistics and inheritance phenomena that could increase the efficiency and precision of crop improvement. In particular, the elucidation of the fundamental mechanisms of heterosis and epigenetics, and their manipulation, has great potential. Eventually, knowledge of the relative values of alleles at all loci segregating in a population could allow the breeder to design a genotype in silico and to practice whole genome selection. High costs currently limit the implementation of genomics-assisted crop improvement, particularly for inbreeding and/or minor crops. Nevertheless, marker-assisted breeding and selection will gradually evolve into 'genomics-assisted breeding' for crop improvement.

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A high density barley microsatellite consensus map with 775 SSR loci.

R. Varshney, T. Marcel, L. Ramsay … (2007)

A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWB(Rec) x OWB(Dom)', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMap 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.

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Author and article information

Contributors

: +91-40-30713305 , +91-40-30713074 , r.k.varshney@cgiar.org

Journal

Journal ID (nlm-ta): Mol Breed

Journal ID (iso-abbrev): Mol. Breed

Title: Molecular Breeding

Publisher: Springer Netherlands (Dordrecht )

ISSN (Print): 1380-3743

ISSN (Electronic): 1572-9788

Publication date (Electronic): 22 November 2011

Publication date PMC-release: 22 November 2011

Publication date (Print): August 2012

Volume: 30

Issue: 2

Pages: 773-788

Affiliations

[1 ]International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324 India

[2 ]Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, 580 005 India

[3 ]Department of Biotechnology, University of Agricultural Sciences, Dharwad, 580 005 India

[4 ]Department of Plant Pathology, University of Agricultural Sciences, Dharwad, 580 005 India

[5 ]Directorate of Groundnut Research (DGR), Junagadh, 362 001 India

[6 ]The University of Georgia, Athens, GA 30602 USA

[7 ]CGIAR-Generation Challenge Programme (GCP), c/o CIMMYT, Mexico, DF 06600 Mexico

Article

Publisher ID: 9661

DOI: 10.1007/s11032-011-9661-z

PMC ID: 3410029

PubMed ID: 22924018

SO-VID: b5648fb5-95f3-4701-bcf9-3378adc74d50

History

Date received : 19 August 2011

Date accepted : 17 October 2011

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ScienceOpen disciplines: Animal science & Zoology

Keywords: genetic linkage map,molecular markers,molecular breeding,rust resistance,late leaf spot resistance

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ScienceOpen disciplines: Animal science & Zoology

Keywords: genetic linkage map, molecular markers, molecular breeding, rust resistance, late leaf spot resistance

Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut ( Arachis hypogaea L.)

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Most cited references 24

Precision mapping of quantitative trait loci.

Genomics-assisted breeding for crop improvement.

A high density barley microsatellite consensus map with 775 SSR loci.

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